Molecular recognition, such as enzymes need to recognize their substrates and drugs have to be designed to specifically bind to certain receptors, is crucial to biology and medicine. Experimentally probing the chemical details of molecular recognition events is challenging, while computer simulations have the potential to provide a detailed picture of such events. We are performing large-scale docking and computer simulations on a group of Periplasmic Binding Proteins aiming to reveal the general relationships between protein structures, its intrinsic dynamics, and mechanism of recognition process.
UROP students will carry out research on modeling protein-ligand interaction. They will use primarily docking software like AutoDock to compute the free energy changes when given molecules bind to their targets. Furthermore, they will interpret the simulation results to address the experimental observations upon interacting with our experimental collaborators. Basic knowledge of physical chemistry and biology is required. Skills in computer science would be a plus.
1. Understand the structure and dynamics of molecules and protein-ligand interactions at the atomic level
2. Learn how to use computational tools for docking and molecular dynamics simulations
3. Learn new knowledge in biophysical chemistry as well as computational structural biology